Have you checked if your pump is hitting the crank...that used to happen to me about once a year, I'd forget why it had happened the time before, and spend an inordinate amount of time looking at my feet. Come to think of it, this was on a 1200D, the predecessor of the 1.2.

It can happen when you apply more pressure because you bend the crank a bit (so doesn't show up when you spin the pedal by hand). There are other things down there that can tap, like the bit of cable jutting out of your front derailleur.

Could be your bottom bracket isn't as tight as it should be - I had the same problem with my Trek last year. Apparently they work loose really easily when brand new, especially if you've been riding lumpy roads. Pop back to the shop and ask them to take a look, unless you've got the right tool to tighten it up yourself.

Bottom Bracket or a pedal bearing would be my guess. If you apply pressure (ie. weight) to the pedal, then there may be a tiny amount of play in the bearing which is causing the clicking noise.

If your bottom bracket is creaking or clicking, then apply some plumbers tape (PTFE Tape) to the bottom bracket threads before re-inserting it. This eliminates any slight movement in the threads which might cause the sound.

i had a prblem with a Trek 1.7c i had the tapping noise from the bottom bracket, i then took it to my local bike shop and they found that the left side of the BB shell hadnt been faced off properly allowing the cup to move sligthly , once this was rectified it stayed tight.
Hope this helps

Tapping problem returned in the bottom bracket.I dont feel any movement through the peddles when the tapping is happening.
I dont want to leave it so that something gets damaged down there so i was thinking about changing the bottom bracket.
But, i dont know firstly what i've got, what i would need to get and how to change it?

I had a tapping noise on my bike last year, I only heard it when I put pressure on the pedals, mainly hill climbing. It only tapped when I moved the pedals around too. It was annoying. The local shop couldn't find anything. Anyway, I took it out in the rain one time, and I've never heard the noise since!